Comet

MS/MS database search

Comet parameter: fragment_bin_offset

This parameter controls how each fragment bin of size fragment_bin_tol
is defined in terms of where each bin starts.

For example, assume a fragment_bin_tol of 1.0. Most intuitively,
the fragment bins would be 0.0 to 1.0, 1.0 to 2.0, 2.0 to 3.0, etc.
This set of bins corresponds to a fragment_bin_offset of 0.0. However,
consider if we set fragment_bin_offset to 0.5; this would cause the
bins to be 0.5 to 1.5, 1.5 to 2.5, 2.5 to 3.5, etc.

So this fragment_bin_offset gives one a mechanism to define
where each bin starts and is centered.

For ion trap data with a fragment_bin_tol of 1.0005,
it is recommended to set fragment_bin_offset to 0.4.

For high-res MS/MS data, one might use a fragment_bin_tol of 0.02
and a corresponding fragment_bin_offset of 0.0.

Allowed values are between 0.0 and 1.0. The actual offset value is
scaled by the fragment_bin_tol value.

I know this is esoteric and any normal user should not give this
parameter any thought beyond using the recommended settings.